A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit--searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair.
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http://dx.doi.org/10.1016/j.dnarep.2014.02.003 | DOI Listing |
J Am Soc Mass Spectrom
January 2025
Department of Chemistry, Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States.
Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) provides direct analytical readouts of small molecules that can be used to characterize the metabolic phenotypes of genetically engineered bacteria. In an effort to accelerate the time frame associated with the screening of mutant libraries, we have developed a high-throughput DESI-MSI analytical workflow implementing a single raster line-scan strategy that facilitates the collection of location-resolved molecular information from engineered strains on a subminute time scale. Evaluation of this "Fast-Pass" DESI-MSI phenotyping workflow on analytical standards demonstrated the capability of acquiring full metabolic profiling information with a throughput of ∼40 s per sample.
View Article and Find Full Text PDFACS Synth Biol
January 2025
Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
Naturally occurring DNA inversion systems play an important role in the generation of genetic variation and adaptation in prokaryotes. Shufflon invertase (SI) from plasmid R64, recognizing asymmetric sites, has been adopted as a tool for synthetic biology. However, the availability of a single enzyme with moderate rates of recombination has hampered the more widespread use of SIs.
View Article and Find Full Text PDFOrg Lett
January 2025
Institute of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan.
Multiple Diels-Alder reactions are a powerful method to construct large asymmetric scaffolds, but these reactions often produce numerous isomers. We now report a triple Diels-Alder reaction between a cyclic furan trimer and -substituted maleimides, achieving selective synthesis of a single asymmetric tris-adduct. The stereoselectivity of cycloaddition to π-extended furan derivatives was clarified by the experimental analysis of intermediates and theoretical calculations.
View Article and Find Full Text PDFJ Phys Chem Lett
January 2025
State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
The Ni-N(His) coordination bond, formed between the nickel ion and histidine residues, is essential for recombinant protein purification, especially in Ni-NTA-based systems for selectively binding polyhistidine-tagged (Histag) proteins. While previous studies have explored its bond strength in a synthetic Ni-NTA-Histag system, the influence of the surrounding protein structure remains less understood. In this study, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to quantify the Ni-N(His) bond strength in calprotectin, a biologically relevant protein system.
View Article and Find Full Text PDFJ Mol Model
January 2025
Applied Nuclear Technology in Geosciences Key Laboratory of Sichuan Province, Chengdu University of Technology, Chengdu, People's Republic of China.
Context: The study of the influence of solvent on 1-bromo adamantane (BAD) exposes prominent solvatochromatic shifts in the optical absorbance and substantial solvent effects on the electronic structure. This facilitates the molecular probe abilities for the BAD with respect to the surrounding environments such as dielectric constant and polarity. BAD exhibits positive solvatochromism for nonpolar solvents and negative solvatochromatic shifts for polar and aromatic solvents.
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